Abstract 6385: Applying NeXT Liquid Biopsy™, an exome-scale platform, to monitor and discover somatic variants in a broad set of cancer types
Authors: Fabio C p Navarro, Naveen Ramesh, Josette Northcott, Rui Chen, Lee D. McDaniel, Charles W. Abbott, Dan Norton, Robin Li, John Lyle, Jason Harris, Gabor Bartha, John West, Sean M. Boyle, Richard O. Chen
Journal: Cancer Research (2022)

Abstract Circulating tumor cell-free DNA (ctDNA) has become a biomarker for prognosis and disease monitoring. However, studies typically utilize assays limited to a small set of genes that may miss biologically important and clinically actionable mutations. To address this limitation, we have developed a whole-exome scale cfDNA platform, NeXT Liquid Biopsy (NeXT LB), that enables sensitive identification of mutations in plasma across ~20,000 genes following interventions such as surgery and treatment therapies. NeXT LB monitors tumor variants and discovers novel mutations in the plasma through analysis of tumor, normal, and plasma samples from the same patient. To enable sensitive detection across the exome in solid tumor and liquid biopsies, we developed an enhanced whole-exome assay and chemistry that augments challenging genomic regions to enable more uniform coverage across the exome. Additionally, we achieve a mean depth of coverage of ~2,000X across the exome, with boosted depth (~5,000X) for 247 clinically relevant oncogenic or tumor suppressor genes to further enhance sensitivity. Finally, we developed computational algorithms to sensitively monitor and discover somatic mutations in liquid biopsies without compromising specificity. In this work, we measure the sensitivity of NeXT LB using SeraCare reference samples with known variants at 0.5%, 1%, and 2% allele fraction (AF). We observe 100% sensitivity at 2% and 1% AF, and &amp;gt;95% sensitivity at 0.5% AF. Additionally, we measure &amp;gt;95% sensitivity for variants with AF &amp;gt;=2% using a proprietary cell-line media system. We generate low-pass Whole Genome Sequencing (lpWGS) data to estimate ctDNA fraction in conjunction with NeXT LB. Considering tumor heterogeneity, NeXT LB is capable of monitoring and discovering somatic variants when lpWGS-reported ctDNA fraction is &amp;gt;=3%, thereby highlighting the performance of the NeXT LB platform. We apply NeXT LB to sequence over 100 matched plasma and normal samples at 250 gigabases (G) and tumors at 50 G. This data demonstrate somatic variation in over 1,000 distinct genes across the cohort, thereby demonstrating the breadth and performance improvements provided by our exome-scale platform in contrast to existing targeted platforms. Additionally, we find that the plasma variants are enriched for higher AFs in solid tumors, thus allowing comprehensive coverage of driver genes and recapitulating hotspots identified in public datasets, including TCGA. We developed an exome-scale NeXT LB technology that enables sensitive monitoring and detection of somatic SNVs and indels from cfDNA. The NeXT LB platform covers a much broader landscape of tumor mutations from the plasma than existing targeted platforms, thereby enabling more comprehensive monitoring and discovery of mutations related to therapies, mechanisms of resistance, intra- and inter-tumor heterogeneity, among others. Citation Format: Fabio C p Navarro, Naveen Ramesh, Josette Northcott, Rui Chen, Lee D. McDaniel, Charles W. Abbott, Dan Norton, Robin Li, John Lyle, Jason Harris, Gabor Bartha, John West, Sean M. Boyle, Richard O. Chen. Applying NeXT Liquid Biopsy™, an exome-scale platform, to monitor and discover somatic variants in a broad set of cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6385.